Doi Lab @ Dept Biosci Info, Keio Univ

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2013

Tokunaga, M., Shiheido, H., Hayakawa, I., Utsumi, A., Takashima, H., Doi, N. (corresponding author), Horisawa, K., Sakuma-Yonemura, Y., Tabata, N., Yanagawa, H. Hereditary spastic paraplegia protein spartin is an FK506-binding protein identified by mRNA Display. Chem. Biol. 20, 935-942 (2013)

Tokunaga, M., Shiheido, H., Tabata, N., Sakuma-Yonemura, Y., Takashima, H., Horisawa, K., Doi, N., Yanagawa, H. MIP-2A is a novel target of an anilinoquinazoline derivative for inhibition of tumor cell proliferation. PLoS ONE 8, e76774 (2013)

土居信英, 柳川弘志. 進化分子工学による新規タンパク質の創出とプロテオミクスへの応用.「進化分子工学～高速分子進化によるタンパク質・核酸の開発～」(伏見譲編) NTS出版, pp. 275-286 (2013)

2012

Sumida, T., Yanagawa, H., Doi, N. In vitro selection of Fab fragments by mRNA display and gene-linking emulsion PCR. J. Nucleic Acids 2012, 371379 (2012)

Shiheido, H., Naito, Y., Kimura, H., Genma, H., Takashima, H., Tokunaga, M., Ono, T., Hirano, T., Du, W., Yamada, T., Doi, N., Iijima, S., Hattori, Y., Yanagawa, H. An anilinoquinazoline derivative inhibits tumor growth through interaction with hCAP-G2, alpha subunit of condensin II. PLoS ONE 7, e44889 (2012)

Shiheido, H., Terada, F., Tabata, N., Hayakawa, I., Matsumura, N., Takashima, H., Ogawa, Y., Du, W., Yamada, T., Shoji, M., Sugai, T., Doi, N., Iijima, S., Hattori, Y., Yanagawa, H. A phthalimide derivative that inhibits centrosomal clustering is effective on multiple myeloma. PLoS ONE 7, e38878 (2012)

Doi, N. (corresponding author), Yamakawa, N., Matsumoto, H., Yamamoto, Y., Nagano, T., Matsumura, N., Horisawa, K., Yanagawa, H. DNA display selection of peptide ligands for a full-length human G protein-coupled receptor on CHO-K1 cells. PLoS ONE 7, e30084 (2012)

Tanaka, J., Yanagawa, H., Doi, N. Evolutionary Engineering of Artificial Proteins with Limited Sets of Primitive Amino Acids. In: Protein Engineering, Kaumaya, P. (Ed.), pp. 59-74, InTech, Rijeka, Croatia (2012)

土居信英. 無細胞提示系による低分子抗体の試験管内進化.「次世代医薬開発に向けた抗体工学の最前線」シーエムシー出版, pp. 66-73 (2012)

2011

Tanaka, J., Yanagawa, H., Doi, N. Comparison of the frequency of functional SH3 domains with different limited sets of amino acids using mRNA display. PLoS ONE 6, e18034 (2011)

Shiheido, H., Takashima, H., Doi, N. (corresponding author), Yanagawa, H. mRNA display selection of an optimized MDM2-binding peptide that potently inhibits MDM2-p53 interaction. PLoS ONE 6, e17898 (2011)

Doi, N. (corresponding author), Kakukawa, K., Oishi, Y., Yanagawa, H. High Solubility of Random-Sequence Proteins Consisting of Five Kinds of Primitive Amino Acids. In: Chemical Synthetic Biology, Luisi, L. and Chiarabelli, C. (Eds.), pp. 121-137, A John Wiley & Sons, UK (2011)

2010 （IN 堀澤健一；OUT 柳川弘志）

Matsumura, N., Tsuji, T., Sumida, T., Kokubo, M., Onimaru, M., Doi, N., Takashima, H., Miyamoto-Sato, E., Yanagawa, H. mRNA display selection of a high-affinity, Bcl-XL-specific binding peptide. FASEB J. 24, 2201-2210 (2010)

Tanaka, J., Doi, N. (co-corresponding author), Takashima, H., Yanagawa, H. Comparative characterization of random-sequence proteins consisting of 5, 12 and 20 kinds of amino acids. Protein Sci. 19, 786-795 (2010)

Chiku, M., Horisawa, K., Doi, N., Yanagawa, H., Einaga, Y. Electrochemical detection of tyrosine derivatives and protein tyrosine kinase activity using boron-doped diamond electrodes. Biosens. Bioelectron. 26, 235-240 (2010

柳川弘志, 土居信英. 生体高分子の進化工学.「現代生物科学入門９：合成生物学」岩波書店, pp. 1-34 (2010)

2009

Sumida, T., Doi, N. (co-corresponding author), Yanagawa, H. Bicistronic DNA display for in vitro selection of Fab fragments. Nucleic Acids Res. 37, e147 (2009)

Tsuji, T., Onimaru, M., Doi, N., Miyamoto-Sato, E., Takashima, H., Yanagawa, H. In vitro selection of GTP-binding proteins by block shuffling of estrogen-receptor fragments. Biochem. Biophys. Res. Commun. 390, 689-693 (2009)

Tabata, N., Sakuma, Y., Honda, Y., Doi, N., Takashima, H., Miyamoto-Sato, E., Yanagawa, H. Rapid antibody selection by mRNA display on a microfluidic chip. Nucleic Acids Res. 37, e64 (2009)

Horisawa, K., Imai, T., Okano, H., Yanagawa, H. 3'-Untranslated region of doublecortin mRNA is a binding target of the Musashi1 RNA-binding protein. FEBS Lett. 583, 2429-2434 (2009)

FANTOM Consortium, Suzuki, H., Forrest, A.R., van Nimwegen, E., Daub, C.O., Balwierz, P.J., Irvine, K.M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M.J., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., Asada, M., Asahara, H., Bailey, T., Bajic, V.B., Bauer, D., Beckhouse, A.G., Bertin, N., Björkegren, J., Brombacher, F., Bulger, E., Chalk, A.M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engström, P.G., Essack, M., Faulkner, G.J., Fink, J.L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S.M., Gustafsson, M., Hashimoto, M., Hashimoto, T., Hatakeyama, M., Heinzel, S., Hide, W., Hofmann, O., Hörnquist, M., Huminiecki, L., Ikeo, K., Imamoto, N., Inoue, S., Inoue, Y., Ishihara, R., Iwayanagi, T., Jacobsen, A., Kaur, M., Kawaji, H., Kerr, M.C., Kimura, R., Kimura, S., Kimura, Y., Kitano, H., Koga, H., Kojima, T., Kondo, S., Konno, T., Krogh, A., Kruger, A., Kumar, A., Lenhard, B., Lennartsson, A., Lindow, M., Lizio, M., Macpherson, C., Maeda, N., Maher, C.A., Maqungo, M., Mar, J., Matigian, N.A., Matsuda, H., Mattick, J.S., Meier, S., Miyamoto, S., Miyamoto-Sato, E., Nakabayashi, K., Nakachi, Y., Nakano, M., Nygaard, S., Okayama, T., Okazaki, Y., Okuda-Yabukami, H., Orlando, V., Otomo, J., Pachkov, M., Petrovsky, N., Plessy, C., Quackenbush, J., Radovanovic, A., Rehli, M., Saito, R., Sandelin, A., Schmeier, S., Schönbach, C., Schwartz, A.S., Semple, C.A., Sera, M., Severin, J., Shirahige, K., Simons, C., St Laurent, G., Suzuki, M., Suzuki, T., Sweet, M.J., Taft, R.J., Takeda, S., Takenaka, Y., Tan, K., Taylor, M.S., Teasdale, R.D., Tegnér, J., Teichmann, S., Valen, E., Wahlestedt, C., Waki, K., Waterhouse, A., Wells, C.A., Winther, O., Wu, L., Yamaguchi, K., Yanagawa, H., Yasuda, J., Zavolan, M., Hume, D.A.; Riken Omics Science Center, Arakawa, T., Fukuda, S., Imamura, K., Kai, C., Kaiho, A., Kawashima, T., Kawazu, C., Kitazume, Y., Kojima, M., Miura, H., Murakami, K., Murata, M., Ninomiya, N., Nishiyori, H., Noma, S., Ogawa, C., Sano, T., Simon, C., Tagami, M., Takahashi, Y., Kawai, J., Hayashizaki, Y. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat. Genet. 41, 553-562 (2009)

Kosugi, S., Hasebe, M., Tomita, M., Yanagawa, H. Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs. Proc. Natl. Acad. Sci. USA 106, 10171-10176 (2009)

Kosugi, S., Hasebe, M., Matsumura, N., Takashima, H., Miyamoto-Sato, E., Tomita, M., Yanagawa, H. Six classes of nuclear localization signals specific to different binding grooves of importin alpha. J. Biol. Chem. 284, 478-485 (2009)

2008

Horisawa, K., Doi, N., Yanagawa, H. Use of cDNA tiling arrays for identifying protein-interactions selected by in vitro display technologies. PLoS ONE 3, e1646 (2008)

Tsuji, T., Nagata, T., Yanagawa, H. N- and C-terminal fragments of a globular protein constructed by elongation of modules as units associated for functional complementation. J. Biochem. 144, 513-521 (2008)

Kosugi, S., Hasebe, M., Entani, T., Tateyama, S., Tomita, M., Yanagawa, H. Design of peptide inhibitors for the importin a/b nuclear import pathway by activity-based profiling. Chem. Biol. 15, 940-949 (2008)

Kosugi, S., Hasebe, M., Tomita, M., Yanagawa, H. Nuclear export signal consensus sequences defined using a localization-based yeast selection system. Traffic 9, 2053-2062 (2008)

2007

Doi, N., Takashima, H., Wada, A., Oishi, Y., Nagano, T., Yanagawa, H. Photocleavable linkage between genotype and phenotype for rapid and efficient recovery of nucleic acids encoding affinity-selected proteins. J. Biotechnol. 131, 231-239 (2007)

Nishizaki, T., Tsuge, K., Itaya, M., Doi, N., Yanagawa, H. Metabolic engineering of carotenoid biosynthesis in Escherichia coli by ordered gene assembly in Bacillus subtilis (OGAB). Appl. Environ. Microbiol. 73, 1355-1361 (2007)

Kawahashi, Y., Doi, N., Oishi, Y., Tsuda, C., Takashima, H., Baba, T., Mori, H., Ito, T., Yanagawa, H. High-throughput fluorescence labeling of full-length cDNA products based on a reconstituted translation system. J. Biochem. 141, 19-24 (2007)

土居信英. エマルジョン法.「ナノバイオ大事典」テクノシステム (2007)

堀澤健一, 土居信英. インヴィトロウイルス法.「ナノバイオ大事典」テクノシステム (2007)

2006

Oishi, Y., Yunomura, S., Kawahashi, Y., Doi, N., Takashima, H., Baba, T., Mori, H., Yanagawa, H. Escherichia coli proteome chips for detecting protein-protein interactions. Proteomics 6, 6433-6436 (2006)

Fukuda, I., Kojoh, K., Tabata, N., Doi, N., Takashima, H., Miyamoto-Sato, E., Yanagawa, H. In vitro evolution of single-chain antibodies using mRNA display. Nucleic Acids Res. 34, e127 (2006)

Oyama, R., Takashima, H., Yonezawa, M., Doi, N., Miyamoto-Sato, E., Kinjo, M., Yanagawa, H. Protein-protein interaction analysis by C-terminally specific fluorescence labeling and fluorescence cross-correlation spectroscopy. Nucleic Acids Res. 34, e102 (2006)

Tateyama, S., Horisawa, K., Takashima, H., Miyamoto-Sato, E., Doi, N., Yanagawa, H. Affinity selection of DNA-binding protein complexes using mRNA display. Nucleic Acids Res. 34, e27 (2006)

Matsumura, N., Doi, N., Yanagawa, H. Recent progress and future prospects in protein display technologies as tools for proteomics. Curr. Proteomics 3, 199-215 (2006)

Tsuji, T., Onimaru, M., Yanagawa, H. Towards the creation of novel proteins by block shuffling. Comb. Chem. High Throughput Screen. 9, 259-269 (2006)

Miyamoto-Sato, E., Yanagawa, H. Toward functional analysis of protein interactome using "in vitro virus": in silico analyses of Fos/Jun interactors. J. Drug Target. 14, 505-511 (2006)

Miyamoto-Sato, E., Yanagawa, H. Puromycin technology for proteome exploration using cell-free translation systems. Recent Devel. Nucleic Acids Res. 2, 163-173 (2006)

Mizutani, T., Fukushi, S., Iizuka, D., Inanami, O., Kuwabara, M., Takashima, H., Yanagawa, H., Saijo, M., Kurane, I., Morikawa, S. Inhibition of cell proliferation by SARS-CoV infection in Vero E6 cells. FEMS Immunol. Med. Microbiol. 46, 236-243 (2006)

2005

Doi, N., Kakukawa, K., Oishi, Y., Yanagawa, H. High solubility of random-sequence proteins consisting of five kinds of primitive amino acids. Protein Eng. Des. Sel. 18, 279-284 (2005)

Horisawa, K., Doi, N., Takashima, H., Yanagawa, H. Application of quantitative real-time PCR for monitoring the process of enrichment of clones on in vitro protein selection. J. Biochem. 137, 121-124 (2005)

Ijima, Y., Matoishi, K., Terao, Y., Doi, N., Yanagawa, H., Ohta, H. Inversion of enantioselectivity of asymmetric biocatalytic decarboxylation by site-directed mutagenesis based on the reaction mechanism. Chem. Commun. 7, 877-879 (2005)

Miyamoto-Sato, E., Ishizaka, M., Horisawa, K., Tateyama, S., Takashima, H., Fuse, S., Sue, K., Hirai, N., Masuoka, K., Yanagawa, H. Cell-free co-translation and selection using in vitro virus for high-throughput analysis of protein-protein interactions and complexes. Genome Res. 15, 710-717 (2005)

Kitagawa, N., Washio, T., Kosugi, S., Yamashita, T., Higashi, K., Yanagawa, H., Higo, K., Satoh, K., Ohtomo, Y., Sunako, T., Murakami, K., Matsubara, K., Kawai, J., Carninci, P., Hayashizaki, Y., Kikuchi, S., Tomita, M. Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). Bioinformatics 21, 1758-1763 (2005)

土居信英, 柳川弘志. マイクロカプセルを利用した制限酵素および受容体リガンドの試験管内選択法. Bioテクノロジー・ジャーナル 1, 84-86 (2005)

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1997-2004

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